feature request checkbed

[Stéphane Plaisance]

Hi Aaron,

Would it be possible to add such a command to bedtools to diagnose all possible erroneous records and put them in a file or on screen.
A curative mode would even be nicer, cleaning the file at the same time as storing the error triggering lines.
I from time to time get errors while running bedtools commands that relate to wrong delimiters (not anymore ;-) ) or 'end less than start'.
I made a primitive and quite inefficient bash script to isolate the later after generating start=0 lines by liftover.

Thanks
Stephane

###
checkbed ()
{
# does not check for other IFS than 'tab'
if [[ $1 == *.bed.gz ]]; then
name=$(basename $1 ".bed.gz");
zcat $1 | gawk –v name=${name} 'BEGIN{FS="\t"; OFS="\t"}
{if ($2==0 || $3<$2) print $0>name"-errors.bed"; else print $0; }'
else
name=$(basename name ".bed");
cat $1 | gawk –v name=${name} 'BEGIN{FS="\t"; OFS="\t"}
{if ($2==0 || $3<$2) print $0>name"-errors.bed"; else print $0; }'
fi
}

[Aaron Quinlan]

Hi Stephane,

I recognize the general utility of having validation tool.  However, I feel this is somewhat low priority, as the tools themselves will identify the exact cause of many common problems.  As such, we may consider something like this for a future release, but I would have to consider it somewhat low priority given our current development goals.

Thanks for the suggestion,

- Aaron

quinlanlab.org